Error - 'Invoice reference number has already been used' when changing the invoice reference for a purchase invoice in the batch

The problem is caused by a setting in the Purchase Ledger Options which can be disabled as follows:

Click System, Options.
Click Purchase Ledger Options.
Click Edit.
Clear the Prevent Duplicate Purchase Invoice Numbers check box.
To commit the change, click Save.
After making the change to the Invoice Number in the batch it is recommended to reset the option to prevent other duplicates being entered.